As has been announced recently on the home page of this year’s BOSC (the Bioinformatics Open Source Conference) and as I just posted on the O|B|F News, Julian Lombardi will be giving the keynote address this year at the conference.
I am serving …

http://bioperl.org/mailman/listinfo/bioperl-l

BTW, Bio::Tools::Run::Phylo::PAML::Yn00/codeml were recently updated to deal with results from PAML 3.15 which could be your problem, but you’ll have to update from CVS.

what’s happen??

use lib “/usr/local/lib/perl5/site_perl/5.8.7″;
use Bio::Tools::Run::Phylo::PAML::Yn00;
use Bio::AlignIO;
my $alignio = new Bio::AlignIO(-format => ‘phylip’,
-file => ‘/r1/people/daewon_kim/ Oranutan_cDNA/2.Processing/4.CodonC/dNdSGene1.phylip’,

-idlength=>12,
-interleaved => 1);
my $aln = $alignio->next_aln;

my $yn = new Bio::Tools::Run::Phylo::PAML::Yn00();
$yn->alignment($aln);
my ($rc,$parser) = $yn->run();

if(my $result = $parser->next_result) {
my @otus = $result->get_seqs();
my $MLmatrix = $result->get_MLmatrix();
# 0 and 1 correspond to the 1st and 2nd entry in the @otus array
my $dN = $MLmatrix->[0]->[1]->{dN};
my $dS = $MLmatrix->[0]->[1]->{dS};
my $kaks =$MLmatrix->[0]->[1]->{omega};
print “Ka = $dN Ks = $dS Ka/Ks = $kaks\n”;
}

I think what is best is to add some of these comments to the module page on the wiki when someone has time so we can build a todo list on that page which everyone can edit and update when finished.

I have been trying to order nodes by similarity and the method ‘height’ works very well in most instances. It would be nice to have a ‘revheight’ method as well. I presume that the two methods would be similar to the “Ladderise” left and right from TreeView.

I also think that it would be useful to have a leaf ordering algorithm similar to the one published by Bar-Joseph Z, Gifford DK and Jaakkola TS.Fast optimal leaf ordering for hierarchical clustering. Bioinformatics. 2001;17 Suppl 1:S22-9.

Also I promoted you to author so you can post news I think.

Also, any reason why comments need to be approved?  I tried posting several times and got nothing, but then I checked the coments section of this page when I logged in and (voila!) there they are!